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Companion Website
Sansom & Horton: Internet for Molecular Biologists
Chapter 07
| Overview Resources for internet collaboration |
A companion web page to internet collaboration, Chapter 10, In: The Internet for molecular biolotists, Oxford University Press, Oxford, 2002 | http://www.internetbiologists.org/collaboration/ |
| Challenges of Internet
Collaboration Schrage, M. Concepts of collaboration |
Shared Spaces as Collaborative Tools. Information TEchnology 'summIT'. (Internet Archive March 10, 2000) | http://web.archive.org/web/20000310033144/www.dtic.mil/summit/ma01.html |
| Schrage M. Leading lights: Technology Designer Michael Schrage | Interview | http://www.webcom.com/quantera/schrage.html |
| Asynchronous communications and
E-mail Multipurpose internet mail extensions (MIME) |
MIME extends the format of internet mail to allow non-US-ASCII textual messages, non-textual messages, multipart messaging bodies, and non-US-ASCII information in message headers | http://www.oac.uci.edu/indiv/ehood/MIME/MIME.html |
| Eudora version 5.2 | E-mail client from Qualcomm | http://www.eudora.com/ |
| Wincode Encoder/Decoder | Freeware utility supporting UUencode, BASE64, BinHex and other formats for Windows 3.x and 95 | http://www.winsite.com Enter search for wincode |
| In a Nutshell. Using wincode | Unofficial tips (and alternate download for wincode) | http://www.telecommunications.com/nutshell/wincode.htm |
| Pretty Good Privacy (PGP) Freeware | MIT Distribution Center for PGP cryptographic software | http://web.mit.edu/network/pgp.html |
| Mail Lists LISTSERV |
Commercial maling list management software (list server) | http://listserv.acsu.buffalo.edu |
| Majordomo | Another widely used list server favoured by internet biologists (IB) | http://www.greatcircle.com/majordomo |
| CataList reference site | Official catalogue of LISTSERV lists (75,353 lists available) | http://www.lsoft.com/catalist.html |
| Lyris.net | E-mail marketing resource guide. Link to LIstManager list server | http://www.lyris.net/ |
| QuickTopic.com | Create a hosted single topic discussion list (bulletin board) | http://www.quicktopic.com |
| QuickTopic document review | A private space for consolidating comments from collaborators on an HTML or Word document under review | http://www.quicktopic.com/cgi-bin/docreviewintro.cgi |
| Topica | Manage and participate in e-mail discussion lists (free membership registration). There are currently 49 biology discussion groups. Topica acquired Liszt Newsgroups but does not support newsgroups. | http://www.topica.com |
| Newsgroups and
Bionet GoogleGroups |
Search and brose Usenet discussion forums (formerly DejaNews) | http://groups.google.com |
| BioSci | Set of electronic communications forums (bionet newsgroups and parallel e-mail lists) used by biological scientists worldwide | http://www.bio.net |
| BioSci bionet Newsgroup archives | Advertising on this site supports newsgroup maintenance | http://www.bio.net |
| Marcato, D. Host a Discussion Forum with the Windows 2000 NNTP Service | News server software built into Windowns 2000. May be installed at time of operating system installation or at a later time. | http://www.microsoft.com/mind/0100/NNTP.NNTP.asp |
| Synchronous communications and shared tools
and Internet chatrooms and whiteboards ZDNet |
A convenient source of software reviews and downloads for Internet tools | http://www.zdnet.com/ |
| Groupboard.com | Install a collaborative whiteboard, chat or message board on your web page. Demo available. | http://www.groupboard.com |
| ICQ homepage | Acronym intended to sound like 'I Seek You'. Prototypic instant messenger software with many features. Allows private messaging, but like most IM systems the Interest Groups are not professionally oriented. | http://web.icq.com |
| Yahoo! Messenger | Instant messenger from the Yahoo family of Internet services. | http://messenger.yahoo.com |
| AIM | A widely used instant messenger for AOL customers | http://www.aim.com |
| MSN Messenger for Windows | Another instant messenger from Microsoft | http://messenger.microsoft.com |
| Cerulean Studios Trillian Pro | An instant messenger client intended to provide interoperability with other systems | http://www.ceruleanstudios.com/trillian/index.html |
| Jabber Software Foundation | An instant messenger protocol designed to provide interoperability | http://www.jabber.org |
| Integrated websites Yahoo! Groups |
Everything in one site for mail lists, file sharing, chat, etc., was called eGroups before becoming part of the Yahoo family of services. A favorite of IB. | http://www.groups.yahoo.com |
| Intranets.com | A commercial all-in-one collaboration site with many features | http://www.intranets.com |
| Blackboard.com | Develop a free online course with many features. Commercial versions of this courseware are widely used by universities and colleges. (There are many other courseware products and hosted services.) | http://company.blackboard.com/courses/index.htm |
| Multi-user virtual
environments LambdaMOO |
The prototypic Multi-user Object Oriented (MOO) collaborative environment | http://trace.ntu.ac.uk/community/Lambda.htm |
| MOO home page | Links to MOO resources | http://www.moo.mud.org |
| LambdaMOO's Programmer Manual (April 1996) | Resources for building in a LambdaMOO-based environment | http://www.bvu.edu/ctown/Progman/ProgrammersManual_Toc.html |
| WebDeveloper.com. VRML | Virtual Reality Modeling Language (VRML) resource | http://www.webdeveloper.com/vrml/ |
| BioMOO home page (now defunct--see web archive) | Past example of a premier biology community online (Internet Archive February 24, 1999). BioMOO was the collaborative home of IB and many other biology collaborations until 2002. | http://web.archive.org/web/19990224020349/ http://bioinformatics.weizmann.ac.il/biomoo/ |
| BioMOO: Teaching Biology in Virtual Reality by Clare Sansom | An article on teaching in a MOO environment, based on the now defunct BioMOO | http://science.uniserve.edu.au/mirror/vCUBE97/html/clare_sansom.html |
| Diversity University (DU) at DU Educational Technology Services, Inc. (non-profit educational organization) | A collaborative MOO currently used by IB. DU hosted IB online lectures and discussions for its 'Perl for Biologists' course in 2002-2003. | http://www.du.org |
| IB MOO Guide for DU by Zev Leifer | Describes the options for connecting to DU and accessing the IB classroom | http://www.ib-perl.org/class/MOO/MOOguide.html |
| Collaborative Virtual Workspace (CVW) | Find information on the open source CVW prototype collaborative environment. This 'pre-built' MOO environment based on LambdaMOO was developed by Mitre Corporation and released to the public domain. | http://cvw.souceforge.net/cvw/info/CVWOverview.php3 |
| SourceForge | Official site for open source software | http://sourceforge.net |
| SjSWorld Community Forum | Instant Messaging simply explained | http://publ69.ezboard.com/fsjsworldforumsfrm7.showMessage?topicID=1.topic |
| Other real-time tools Conferencing on the Web by David R. Wooley |
Categorized listing of software for Internet discussion and collaboration | http://thinkofit.com/webconf/index.htm |
| ConferZone | Resource Center, Newsletter, and Vendor Information | http://www.conferzone.com/ |
| CollabTools | Listing of tools for Internet collaboration | http://www.voght.com/cgi-bin/pywiki?CollabTools |
| Microsoft Windows Technologies Windows NetMeeting | Windows software for online collaborative meetings. Supports A/V conferencing, whiteboard, chat, and file sharing. Comes with Windows 2000. | http://www.microsoft.com/windows/NetMeeting/Features/default.ASP |
| pcAnywhere | Symantec's remote control software. May be useful in controlling collaborative applications on another computer and for file transfers. | http://enterprisesecurity.symantec.com/products/products.cfm?productID=2 |
| Community of Science (COS) | Various tools to assist professional scientists and soceities. Access to databases of funding information, experts, and online reference databases through the COS Workbench | http://www.cos.com |
| COS Abstract Management System | COS Abstract Management System is suitable for managing review of abstracts for scientific societies. A demonstration is available. | http://ams.cos.com/demo/overview/shtml |
| EPanel from Humanitas. The On-Line Panel Evaluation Website. | Software for collaborative panel evaluations. In use by government agencies. Supports Windows and Macintosh | http://www.epanel.cc/ |
| NIH VideoCasting at the NIH Center for Information Technology (CIT) | What is NIH VideoCasting | http://videocast.nih.gov/videocastinfo.asp |
| NIH VideoCasting | Direct access to NIH current events and archived scientific lectures on video | http://videocast.nih.gov/ |
| Usability First. Your online guide to usability resources | Link to groupware resources | http://www.usabilityfirst.com/ |
| Udell, John. Internet Groupware for scientific collaboration | In depth guide to groupware for scientific collaboration (ca 2000) | http://udell.roninhouse.com/GroupwareReport.html |
| Courses IB Homepage |
A small international online comunity of biologists that pursues educational and research collaborations using Internet tools and resources | http://www.internetbiologists.org/ |
| BRI course homepage (now defunct--see web archive) | BRI is Internet Biologists first course and has had several international editions introducing the use of the Internet to biologists (Web archive 23 January, 2001) | http://web.archive.org/web/20010123085400 http://www.internetbiologists.org/bri99.index.html |
| BRI course content (now defunct--see web archive)
DBRI course homepage (now defunct--see web archive) |
Description of BRI course content (Web archive
21 April, 2001) DBRI is Internet Biologists advanced course covering topics for Internet-based research (e.g. collaborative systems, sequence-based analyses, molecular visualization, virtual laboratories). There have been several international editions. (Web archive 7 October, 2001.) |
http://web.archive.org/web/20010421090738/www.netbio.org/bri99/content.html DBRI course homepage (now defunct--see web archive)">http://web.archive.org/web/20011007083707/http://www.internetbiologists.org/dbri99/ |
| Perl for biologists homepage | IB most recent online course introducing the PERL scripting language from the basics to bioinformatics applications. The first edition in 2002-2003 consisted of lectures/discussions, web resources, and exercises | http://www.ib-perl.org |
| Lau, C.H., Leifer, Z., Kossida, S., and I.R. Schaffner, Jr. (1997). BRI: a model solution for remaining current on Internet resources and technology. Presented at the Virtual Conference on Computers in University Biology Education | An early article about the BRI course that was the beginning of IB | http://science.uniserve.edu.au/mirror/vCUBE97/html/chin_hoon_lau.htm |
| Order out of chaos: organizing your Internet searches by Zev Leifer | A lecture from the IB BRI course | http://emile-21.com/BRI/BRI97_transcript_19970619.html |
| Course: Principles of protein structure | A course presented by the Department of Crystallography, Birkbeck College, University of London | http://www.cryst.bbk.ac.uk/PPS2/top.html |
| Biocomputing hypertext coursebook (1996) | Workbook from online course given by the Virtual School of Natural Sciences (VSNS)--BioComputing Division, University of Bielefeld | http://www.techfak.uni-bielefeld.de/bcd/Curric/welcome.html |
| Course: Structure-Based Drug Design (defunct site--see web archive) | Certificate/diploma course given by the Virtual School of Molecular Sciences, University of Nottingham (ca 1997) (Web archive 6 December, 2000) | http://web.archive.org/20001206143600/ http://www.vsms.nottingham.ac.uk/vsms/s bdd/index.html |
| The Genome Web. Bioinformatics Course Information | UK Human Genome Mapping Project Resource Centre | http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinf-course-info.html |
| Conferences Glycoscience Conference |
Sponsored by Eurotron, presented by Netconferences. A meeting of glycoscience researchers | http://www.netconferences.net/eurotron |
| Virtual Conference on Computers in University Biology Education (Virtual CUBE97) | An online conference sponsored by CTI Biology, University of Liverpool | http://science.uniserve.edu.au/mirror/vCUBE97/home.html |
| Laboratories Leifer, Z. (1997). A microbiology office-laboratory in cyberspace |
A paper presented at the vCUBE conference about a virtual microbiology laboratory writeen in MOO language, previously hosted on BioMOO, now reporduced in DU | http://science.uniserve.edu.au/mirror/vCUBE97/html/zev_leifer.html |
| The Cybertory® Virtual Molecular Biology Laboratory. | A web-based virtual laboratory written in JavaScript | http://www.attotron.com/cybertory/ |
| Leifer, Z. Research Collaboration via MOO | An article in HMS Beagle on the use of the MOO format for online research collaboration (Prior rapid, free registration with BioMedNet is required) | http://news.bmn.com/hmsbeagle/24/webres.insitu.htm |
| Virtual Institute of Experimental (Wet) Biology (VIWB) | A venue to publicize member's projects and a call for collaboration. An IB project. | http://www.md.huji.ac.il/biology |
| VIWB Projects | A listing of the members and their projects | http://bioinfo.weizmann.ac.il:3680/porjects.html |
| Globewide Network Academy | Distance learning catalogue and related GNA projects. 31645 courses and 4348 programs listed | http://www.gnacademy.org/ |
| Overcoming distance and language
barriers Language Choice Online: Globalization and Identity in Egypt by M. Warschauer and G.R. El Said |
Cultural factors affecting online language use and translation | http://www.ascusc.org/jcmc/vol7/issue4/warschauer.html |
| Multilingual Internet: language, culture and communication in instant messaging, e-mail and chat. A call for papers | Annoucement in the Journal of Computer-Mediated Communications (at the University of Southern California) | http://www.ascusc.org/jcmc/cfpmultilingual.html |
| Babel Fish, World: translation | One of the first and best online free language translators by AltaVista | http://babelfish.altavista.com/translate.dyn |
| Systran information and translation technologies | Systran software is used by several language translators | http://www.systransoft.com |
| Internet interpreters. CNET Reviews | The CNET site may be searched for reviews of AltaVista Babel Fish, Transparent Language FreeTranslation, and Translation Experts InterTran | http://www.cnet.com/ |
| Open Translation Engine 0.7.9 | Open source project for language translation | http://www.ibiblio.org/dbarberi/ote/stable/ |
| Google language tools | Translate text or web pages | http://www.google.com/language_tools?hl=en |
| Langenberg.com Language Translation | Another online translator for English, French, German, Danish, Spanish, Finnish, Czech and Italian | http://translation.langenberg.com/ |
| WorldLingo.com | Add an online language translator to your browser
(subscription) Conduct multilingual chat in 10 languages (demo available) |
http://www.worldlingo.com/products_services/browser_tool.html http://www.worldlingo.com/products_servic es/chat.html |
| IBM Research. Translation | Description of the IBM web intermediary (WBI) as a language translation plugin, using the FreeTranslation engine as an example | http://www.almaden.ibm.com/cs/wbi/doc/examples/translation/ |
| Language Partners International | Reference Center for foreign language translation | http://languagepartners.com/reference-center/start-here/index.htm |
| Overcoming cultural barriers Lau, C.H. (1998). In Search of Permanency: A Founder's Perspective on Sustainability of Purely Virtual Team |
Article from the founder of IB on virtual teaming | http://emile-21.com/NetBio/permanency.html |
| Collaboration with grid computing A Grid Computing Primer |
Describes the background to grid computing and gives links to other useful resources | http://www.grids-center.org/grids_primer.asp |
| Scientists giddy about the grid by Randy Dotinga. Wired News. 20 January, 2003 | Short article touting the possibilities for grid computing | http://www.wired.com/news/print/0,1294,57265,00.html |
| BIRN. Biomedical Informatics Research Network | Introduces the BIRN initiative and describes the motivation and role of grid infrastructure | http://www.nbirn.net/About/Overview/Objectives.htm |
| Scientific Objectives of the Biomedical Informatics Research Network (BIRN) | Describes exemplary uses of BIRN resources in the field of neuroimaging | http://birn.ncrr.nih.gov/birn/birn_getpage.php?fname=about_birn_bg.html |
| About BioGRID at the National University of Singapore (NUS) | Brief introduction to BioGRID | http://www.bid.nus.edu.sg/biogrid/ |
| Biology Workbench portal at the San Diego Supercomputer Center | A portal that simplifies access to sophisticated biological research tools (registration required) | http://workbench.sdsc.edu/ |